6-57987845-T-A

Position:

• chr6-57987845-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000641775.1(ENSG00000225096):​n.171+25597T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,852 control chromosomes in the GnomAD database, including 6,684 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (6684 hom., cov: 32)
• Consequence: ENST00000641775.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.952

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927293	XR_001744180.1	n.3471+16189T>A		intron_variant, non_coding_transcript_variant
LOC101927293	XR_007059624.1	n.988+16189T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000641775.1	n.171+25597T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43283 AN: 151734 Hom.: 6677 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.286

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.285 AC: 43318 AN: 151852 Hom.: 6684 Cov.: 32 AF XY: 0.278 AC XY: 20660 AN XY: 74270

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.285

Alfa AF: 0.281 Hom.: 831

Bravo AF: 0.290

Asia WGS AF: 0.167 AC: 579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.33
DANN	Benign	0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6934928; hg19: chr6-58314123;